Man pages for epichains
Simulating and Analysing Transmission Chain Statistics Using Branching Process Models
| aggregate.epichains | Aggregate cases in <epichains> objects by "generation" or... |
| covid19_sa | COVID-19 Data Repository for South Africa |
| dborel | Density of the Borel distribution |
| dot-adjust_next_gen | Adjust new offspring if it exceeds the susceptible population... |
| dot-check_generation_time_valid | Check if the generation_time argument is specified as a... |
| dot-check_offspring_func_valid | Check if constructed random number generator for offspring... |
| dot-check_sim_args | Check inputs to 'simulate_chains()' and 'simulate_summary()' |
| dot-check_statistic_args | Check that the 'statistic' and 'stat_threshold' arguments are... |
| dot-check_time_args | Check inputs that control time events |
| dot-complementary_logprob | Calculates the complementary log-probability |
| dot-epichains | Create an <epichains> object |
| dot-epichains_summary | Create an <epichains_summary> object |
| dot-gborel_size_ll | Log-likelihood of the size of chains with gamma-Borel... |
| dot-geom_length_ll | Log-likelihood of the length of chains with geometric... |
| dot-get_statistic_func | Return a function for calculating chain statistics |
| dot-get_susceptible_offspring | Sample the number of susceptible offspring from all possible... |
| dot-init_susc_pop | Adjust next generation vector to match susceptible population... |
| dot-is_epichains | Test if x is an 'epichains' object |
| dot-is_epichains_summary | Test if x is an 'epichains_summary' object |
| dot-nbinom_size_ll | Log-likelihood of the size of chains with Negative-Binomial... |
| dot-new_epichains | Construct an <epichains> object |
| dot-new_epichains_summary | Construct a <epichains_summary> object |
| dot-offspring_ll | Log-likelihood of the summary (size/length) of chains with... |
| dot-pois_length_ll | Log-likelihood of the length of chains with Poisson offspring... |
| dot-pois_size_ll | Log-likelihood of the size of chains with Poisson offspring... |
| dot-rbinom_size | Samples size (the number of trials) of a binomial... |
| dot-rgen_length | Samples chain lengths with given observation probabilities |
| dot-sample_possible_offspring | Sample all possible offspring for the next generation |
| dot-update_chain_stat | Determine and update the chain statistic being tracked |
| dot-validate_epichains | Validate an <epichains> object |
| dot-validate_epichains_summary | Validate an <epichains_summary> object |
| epichains-package | epichains: Simulating and Analysing Transmission Chain... |
| head.epichains | 'head' and 'tail' method for <epichains> class |
| likelihood | Estimate the log-likelihood/likelihood for observed branching... |
| print.epichains | Print an <epichains> object |
| print.epichains_summary | Print an <epichains_summary> object |
| rborel | Generate random numbers from the Borel distribution |
| rgborel | Generate random numbers from a Gamma-Borel mixture... |
| simulate_chains | Simulate transmission chains |
| simulate_chain_stats | Simulate a vector of transmission chains statistics... |
| summary.epichains | Summary method for <epichains> class |
| summary.epichains_summary | Summary method for <epichains_summary> class |
